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<big>'''MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.'''
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=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=
</big>
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[[Image:MSL-logo.png|right|400px]]
 
[[Image:MSL-logo.png|right|400px]]
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'''MSL''' is a open source C++ software library for molecular modeling produced in the [http://seneslab.org '''Senes Lab'''] at the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies.
  
 
===Philosophy===
 
===Philosophy===
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Some of the features supported by the library are:
 
Some of the features supported by the library are:
  
* Support for reading and writing PDB files.
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* Support for reading and writing PDB and CRD files.
 
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
 
* The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
 
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
 
* For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
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* Support for rotamer libraries.
 
* Transformations such as translations, rotations, and alignments.
 
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other potential energies.
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* The CHARMM force field and other energy funtions.
 
* Support for CHARMM topology and parameter files.
 
* Support for CHARMM topology and parameter files.
 
* Structure building from scratch (using internal coordinates)
 
* Structure building from scratch (using internal coordinates)
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===Status===
 
===Status===
Version 1.0 of MSL was released on July 8, 2012, which is suitable for production.
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Current version: 1.1, released on April 3, 2013.
  
The libraries are in an advanced are in active development, and a development version is also available (use it at your own risk).
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Previous versions: 1.0, released on July 8, 2012.
  
 
===Source===
 
===Source===
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* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
 
* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
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* Dan Kulp, Vaccine & Immunotherapy Center, The Wistar Institute and The University of Pennsylvania, PA [https://wistar.org/our-scientists/daniel-kulp, '''Kulp Lab''']
* Jason Donald, Agrivida, Inc., Medford MA
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* Jason Donald, Manus Biosynthesis, Cambridge MA
 
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
 
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
* Gevorg Grigoryan, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']
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* Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']
  
 
=== Reference ===  
 
=== Reference ===  
 
Article published using MSL should cite:
 
Article published using MSL should cite:
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<pubmed>22565567</pubmed>
  
Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G and Senes A
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'''MSL (including early versions) has been used in the following work:'''
"Structural informatics, modeling and design with an open-source Molecular Software Library (MSL)"
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<pubmed>29301955 29233891 29028318 28076776 26702098 26184105 25216398 25212195 24828077 24569864 24003111 23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>
''J. Comput. Chem.'' (2012) '''33(20)''', 1645-61. DOI: 10.1002/jcc.22968
 
[http://dx.doi.org/10.1002/jcc.22968 Download]
 
 
 
'''MSL has been used in the following work:'''
 
<pubmed>22178759 21482808 21321234 21287621 20945900 20080739 19722646</pubmed>
 
<!-- 21287621 -->
 

Latest revision as of 19:39, 29 October 2018

MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.

MSL-logo.png

MSL is a open source C++ software library for molecular modeling produced in the Senes Lab at the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies.

Philosophy

The main goal is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications (protein modeling or design).

The MSL library is not a program (although some applications are distributed) but a tool for scientist to code their own methods.

Features

Some of the features supported by the library are:

  • Support for reading and writing PDB and CRD files.
  • The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
  • For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
  • Support for rotamer libraries.
  • Transformations such as translations, rotations, and alignments.
  • The CHARMM force field and other energy funtions.
  • Support for CHARMM topology and parameter files.
  • Structure building from scratch (using internal coordinates)
  • Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
  • Local backbone sampling.
  • Crystal lattice generation.
  • A PyMOL Python Interface for calling MSL code from within PyMOL.
  • A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
  • And more...

Documentation

The Documentation – currently still under construction – provides a description of the objects and of some distrubuted programs and utilites. A step by step tutorial is being assembled.

Status

Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.

Source

The source code can be downloaded on SourceForge. Go to the Download page. ("To do" list).

Main development team:

  • Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, Senes Lab
  • Dan Kulp, Vaccine & Immunotherapy Center, The Wistar Institute and The University of Pennsylvania, PA Kulp Lab
  • Jason Donald, Manus Biosynthesis, Cambridge MA
  • Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
  • Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, Grigoryan Lab

Reference

Article published using MSL should cite:

Daniel W Kulp, Sabareesh Subramaniam, Jason E Donald, Brett T Hannigan, Benjamin K Mueller, Gevorg Grigoryan, Alessandro Senes
Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).
J Comput Chem: 2012, 33(20);1645-61
[PubMed:22565567] ##WORLDCAT## [DOI] (I p)

MSL (including early versions) has been used in the following work: